[gmx-users] Net charge neutrality during thermodynamic integration

[Michael Shirts]

Try this talk posted on Alchemistry.org by Gabe Rocklin who has carefully
looked at this problem.

http://www.alchemistry.org/wiki/images/5/50/GabrielRocklin2014-PeriodicityArtifacts.pdf

And the full paper:

http://scitation.aip.org/content/aip/journal/jcp/139/18/10.1063/1.4826261



On Sun, Jun 15, 2014 at 2:47 AM, Leandro Bortot <leandro.obt at gmail.com>
wrote:

> Dear users,
>
>      I'm learning how to use the Thermodynamic Integration approach to
> calculate free energy differences. I have done some tutorials, including
> those available at www.alchemistry.org.
>      however, all tutorials I found use neutral ligands for the decoupling.
> Since I use cutoffs with PME and some of my ligands are charged, I wonder
> how should I treat the fact that at labda=1.0 the system net charge will be
> neutral and at lambda=0.0 it will be a non-zero integer value because the
> ligand charges has been set to zero.
>     should I decouple a counter-ion together with the ligand or should I
> let the charge be non neutral and apply some sort of corrections in the
> results?
>
>
>      If possible, could you provide some paper or tutorial in which this is
> done and explained? Although I could find some papers in which charged
> ligands are decoupled, no explanation was given about the net charge.
>
>
> best regards,
> Leandro.
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